I've fitted a Brembo aftermarket radial master cylinder to my KR, works very nicely and is very well made.

Did you have two simple brake hoses fitted? this makes it a little easier bleeding than the original setup of 3 pipes with a splitter.

You could clean out the original master cylinder and fit a new seal kit and brake lever inc pivot bolt if you want to keep it original? They work reasonably well as standard if the bore isn't worn.

If the brake calipers have been cleaned out properly then the new pistons should slide back in the caliper freely and smoothly, try pushing them back to check? I prefer the genuine pistons, is there any difference to the problem if brakes are hot or cold?

When you bleed the lines don't forget to bleed the top banjo bolt as well. Friend of mine spent 2 hours bleeding his brakes and got nowhere. 30 seconds after bleeding the top banjo bolt the lever pressure was perfect

I had a hell of a time bleeding up freshly rebuilt calipers and master cylinder.
The over night cable tie helped, but what made the biggest difference was taking the bike out and generating a lot of heat using it a few times.
It went spongy when cold for a few rides, but ended up feeling very good indeed.

Oh and I got a zxr400 master cylinder, loads about as those pesky kids can't stay upright.
Cheers martin.